A report of 46 unrecorded bacterial species in Korea belonging to the classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria and Epsilonproteobacteria

Abstract

During a comprehensive investigation of indigenous prokaryotic species in Korea, a total of 46 bacterial strains assigned to the classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria were isolated from a diversity of habitats including freshwater, seawater, brackish water, ginseng soil, plant roots, natural caves, and tidal flats. Based on their high 16S rRNA gene sequence similarities (>98.7%) and formation of strongly-supported phylogenetic clades with the closest type species, each strain was assigned to an independent, predefined bacterial species. Since there were no published or official reports regarding the isolation of these 46 species in Korea, here we report them as new species to Korea: 34 species in 14 families in the five orders of Alphaproteobacteria, 10 species in five families in the three orders of Betaproteobacteria, one species of Deltaproteobacteria and one species of Epsilonproteobacteria. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

Introduction

Proteobacteria is the largest bacteria phylum of gramnegative bacteria including the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, Acidithiobacillia and Oligoflexia (Williams et al., 2013; Nakai et al., 2014). At the time of writing, the taxonomic classification based on 16S rRNA sequences shows the class Alphaproteobacteria includes 15 orders: Caulobacterales, Emcibacterales, Iodidimonadales, Kiloniellales, Kordiimonadales, Magnetococcales, Micropepsales, Parvularculales, Pelagibacterales, Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sneathiellales, and Sphingomonadales. Among them, Emcibacterales, Iodidimonadales, and Micropepsales were established within the last three years (Iino et al., 2016; Harbison et al., 2017). The class Betaproteobacteria includes eight orders: Burkholderiales, Ferritrophicales, Gallionellales, Methylophilales, Neisseriales, Nitrosomonadales, Rhodocyclales, and Sulfuricellales. The order Sulfuricellales was established in 2015 (Watanabe et al., 2015). The class Deltaproteobacteria includes nine orders: Bradymonadales, Desulfarculales, Desulfobacterales, Desulfovibrionales, Desulfurellales, Desulfuromonadales, Myxococcales, Nitrospinales, and Syntrophobacterales, and the class Gammaproteobacteria consists of 20 orders: Acidiferrobacterales, Aeromonadales, Alteromonadales, Arenicellales, Cardiobacteriales, Cellvibrionales, Chromatiales, Enterobacterales, Immundisolibacterales, Legionellales, Methylococcales, Nevskiales, Oceanospirillales, Orbales, Pasteurellales, Pseudomonadales, Salinisphaerales, Thiotrichales, Vibrionales, and Xanthomonadales.

In 2017, we collected environmental samples from a diversity of habitats in Korea and isolated many novel and unrecorded bacterial species. This study describes 46 previously unrecorded bacterial species to Korea belonging to the classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria.

Materials and Methods

A total of 46 bacterial strains are assigned to the classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria were isolated from a variety of habitats, including marine algae, mud, red algae, salt plant, salt pond, sand, butterfly (Hippoarchia autonoe), seawater, soil, tidal flat, tree, and wetland (Table 1). All environmental samples were independently processed, serially diluted, spread onto diverse culture agar media including ISP 2 agar(BD, USA), marine agar 2216 (MA; BD, USA), R2A agar (BD, USA), and incubated at 25-37℃ for 2-5 days (Table 1). The designated strain identifications(IDs), isolation sources, culture media, and incubation conditions are described in Table 1. All strains were isolated as pure cultures and stored as 10-20% glycerol suspension at -80℃ and as lyophilized ampoules.

Table 1. Summary of strains isolated belonging to the classes Alphaproteobacteria, Betaproteobacteia, Deltaproteobacteria, and Epsilonproteobacteria and their taxonomic affiliations.

Table 1. Continued.

Colony morphology of the strains was observed by eye or a magnifying glass after the cells were cultivated to their stationary phase on their culture agar media. Cellular morphology and cell size were examined by using either transmission electron or scanning electron microscopy. Gram staining tests were performed using a Gram-staining kit according to the standard procedures. Biochemical characteristics were evaluated by using API 20NE galleries(bioMérieux), according to the manufacturer’s instructions.

Bacterial DNA extraction, PCR amplification, and 16S rRNA sequencing were performed using standard procedures as described elsewhere (Lee et al., 2014). The 16S rRNA sequences of the strains assigned to the classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria were compared with those of valid type strains using the EzTaxon-e server(Kim et al., 2012). For phylogenetic analyses, multiple alignments of the 16S rRNA sequences between the isolates and established bacterial species were carried out using Clustal X (Thompson et al., 1997). Evolutionary distances were calculated using the Kimura two-parameter model and the phylogenetic trees were constructed using a neighbor-joining algorithm with bootstrap values based on 1000 replications(Felsenstein, 2002).

Results and Discussion

Thirty-four strains of Alphaproteobacteria were distributed into five orders: one strain in the Parvularculales, 16 strains in Rhizobiales, 10 strains in Rhodobacterales, three strains in Rhodospirillales, and four strains in Sphingomonadales (Table 1). Ten strains of Betaproteobacteria were distributed into three orders: seven strains in Burkholderiales, two strains in Neisseriales, and one strain in Rhodocyclales. One strain belonged to the order Desulfovibrionales of Deltaproteobacteria and one strain to the order Campylobacterales of Epsilonproteobacteria. All strains were gram-staining-negative and chemoheterotrophic, while in terms of shape, 38 strains were rodshaped, three strains were cocci-shaped, and five strains were ovoid-shaped (Fig. 1).

Fig. 1. Transmission electron micrographs or scanning electron micrographs of cells of the strains isolated in this study. The cells were cultured at their optimal growth conditions. Strains: 1, LPB0183; 2, LPB0211; 3, 17J44-22; 4, 17J27-16; 5, KYW1385; 6, BMW10; 7, IMCC34164; 8, IMCC34184; 9, IMCC34185; 10, IMCC34207; 11, IMCC34233; 12, GH4-12; 13, GH1-7; 14, GH1-10; 15, GH2-6; 16, Ibu_S_3; 17, MMS17- GJ036; 18, MMS17-SY214; 19, Gsoil 1028; 20, Gsoil 1111; 21, Gsoil318-1; 22, Gsoil 824; 23, HMF7612; 24, HMF7644; 25, HMF7868; 26, HMF8042; 27, HMF8046; 28, HMF8205; 29, HMF8467; 30, HMF8483; 31, HMF8486; 32, S-1; 33, F-mm3; 34, StC2; 35, BR3409; 36, JMn9; 37, WD42; 38, kw_8; 39, MMS17-GJ039; 40, Gsoil 096; 41, HMF7346; 42, HMF7693; 43, HMF7887; 44, HMF4721; 45, LPB0172; 46, LPB0305.

In the class of Alphaproteobacteria, one strain was assigned to the genus Parvularcula of the family Parvularculaceae in the order Parvularculales and 16 strains in the order Rhizobiales belonged to seven different families (Fig. 2): Brucellaceae (one strain), Hyphomicrobiaceae (five strains), Aurantimonadaceae (one strain), Parvibaculum (one strain), Phyllobacteriaceae (two strains), Rhizobiaceae (three strains), and Stappia (two strains). Ten strains in the order Rhodobacterales belonged to two families: Hyphomonadaceae (one strain) and Rhodobacteraceae (nine strains). Three strains in the order Rhodospirillales were separated into two families: Acetobacteraceae (one strain) and Rhodospirillaceae (two strains). Lastly, four strains in the order Sphingomonadales were separated into two families: Erythrobacteraceae (two strains) and Sphingomonadaceae (two strains)(Fig. 3).

Fig. 2. Neighbor-joining phylogenetic tree, based on 16S rRNA sequences, showing the phylogenetic relationship between strains isolated in this study and their relatives in the orders Parvularculales and Rhizobiales in the class Alphaproteobacteria. Burkholderia dabaoshanensis GIMN1.004^T (FJ210816) was used as an outgroup. Bootstrap values (>70%) are shown above nodes. Scale bar: 0.02 changes per nucleotide.

Fig. 3. Neighbor-joining phylogenetic tree, based on 16S rRNA sequences, showing the phylogenetic relationship between strains isolated in this study and their relatives in the orders Rhodobacterales, Rhodospirillales, and Sphingomonadales in the class Alphaproteobacteria. Burkholderia dabaoshanensis GIMN1.004^T (FJ210816) was used as an outgroup. Bootstrap values (>70%) are shown above nodes. Scale bar: 0.02 changes per nucleotide.

Ten strains were distributed into three orders, Burkholderiales, Neisseriales, and Rhodocyclales, of the class Betaproteobacteria. Seven strains belonged to three fam-ilies in the order of Burkholderiales: Burkholderiaceae (five strains), Oxalobacteraceae (one strain) and Ralstoniaceae (one strain) (Fig. 4). Two strains belonged to the genera Neisseria and Amantichitinum of the family Neisseriaceae of the order Neisseriales, respectively and one strain belonged to the genus Uliginosibacterium of the family of Rhodocyclaceae in the order Rhodocyclales(Fig. 4). One strain was assigned to the genus Halodesulfovibrio of the family Desulfovibrionaceae in the order Desulfovibrionales and one strain was assigned to the genus Arcobacter of the family Campylobacteraceae in the order Campylobacterales(Figs. 5 and 6).

Fig. 4. Neighbor-joining phylogenetic tree, based on 16S rRNA sequences, showing the phylogenetic relationship between strains isolated in this study and their relatives in the orders Burkholderiales, Neisseriales, and Rhodocyclales in the class Betaproteobacteria. Parvularcula oceanus JLT2013^T (JPHU01000026) was used as an outgroup. Bootstrap values (>70%) are shown above nodes. Scale bar: 0.02 changes per nucleotide.

Fig. 5. Neighbor-joining phylogenetic tree, based on 16S rRNA sequences, showing the phylogenetic relationship between strain LPB0172 isolated in this study and its relatives in the order Desulfovibrionales in the class Deltaproteobacteria. Burkholderia dabaoshanensis GIMN1.004^T (FJ210816) was used as an outgroup. Bootstrap values (>70%) are shown above nodes. Scale bar: 0.05 changes per nucleotide.

Fig. 6. Neighbor-joining phylogenetic tree, based on 16S rRNA sequences, showing the phylogenetic relationship between strain LPB0305 isolated in this study and its relatives in the order Campylobacterales in the class Epsilonproteobacteria. Burkholderia dabaoshanensis GIMN1.004^T (FJ210816) was used as an outgroup. Bootstrap values (>70%) are shown above nodes. Scale bar: 0.02 changes per nucleotide.

In conclusion, we report 46 previously unrecorded bacterial species to Korea belonging to four proteobacterial classes Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria.

Description of Pseudovibrio ascidiaceicola LPB0183

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, smooth, mucoid, and cream-colored after three days of incubation at 25°C on MA. Positive for nitrate reduction, indole production, glucose fermentation, and gelatinase and β-galactosidase activity. Negative for arginine dihydrolase and urease activity and esculin hydrolysis. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain LPB0183 (=VYWGBAC000000035) was isolated from a seawater sample, Jeju, Korea.

Description of Parvibaculum hydrocarboniclasticum LPB0211

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, smooth, and creamcolored after three days of incubation at 25℃ on MA. Negative for nitrate reduction, indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain LPB0211 (=VYWGBAC 000000044) was isolated from a seawater sample, Incheon, Korea.

Description of Rhizobium herbae 17J44-22

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, smooth, and creamcolored after four days of incubation at 25°C on R2A agar. Positive for esculin hydrolysis and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Negative for nitrate reduction, indole production, and glucose fermentation. Utilizes d-glucose, d-mannose, d-maltose, potassium gluconate and malic acid. Does not utilize l-arabinose, d-mannitol, N-acetyl-glucosamine, capric acid, adipic acid, trisodium citrate and phenylacetic acid. Strain 17J44-22 (=VYWGBAC000000379) was isolated from a soil sample, Jeju, Korea.

Description of Devosia submarina 17J27-16

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, smooth, and cream-colored after four days of incubation at 25℃ on R2A agar. Positive for nitrate reduction, esculin hydrolysis, and arginine dihydrolase, urease, and β-galactosidase activity. Negative for indole production, glucose fermentation, and gelatinase activity. Utilizes d-Glucose, larabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, and potassium gluconate. Does not utilize capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain 17J27-16 (=VYWGBAC000000397) was isolated from a soil sample, Jeju, Korea.

Description of Paracoccus tibetensis KYW1385

Cells are gram-staining-negative, non-flagellated, and short rod-shaped. Colonies are circular, convex, smooth, entire, and pale yellow-colored after three days of incubation at 25℃ on MA. Positive for esculin hydrolysis. Negative for nitrate reduction, ndole production, glucose fermentation, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain KYW1385 (=VYWGBAC000000159) was isolated from a seawater sample, Gwangyang, Korea.

Description of Roseobacter litoralis BMW10

Cells are gram-staining-negative, flagellated, and ovoidshaped. Colonies are circular, convex, smooth, opaque, and pale pink red-colored after five days of incubation at 25℃ on MA. Positive for esculin hydrolysis. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain BMW10 (=VYWGBAC000000160) was isolated from a seawater sample, Boseong, Korea.

Description of Devosia pacifica IMCC34164

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, entire, convex, and pale white-colored after three days of incubation at 25℃ on R2A agar using seawater. Positive for esculin hydrolysis and urease and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase and gelatinase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate and phenylacetic acid. Strain IMCC34164 (=VYWGBAC000000116) was isolated from a tidal flat sample, Incheon, Korea.

Description of Ahrensia kielensis IMCC34184

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, entire, convex, and pale white-colored after five days of incubation at 25℃ on R2A agar using seawater. Positive for esculin hydrolysis and urease and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase and gelatinase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain IMCC34184 (=VYWGBAC000000113) was isolated from a tidal flat sample, Incheon, Korea.

Description of Litorimonas cladophorae IMCC34185

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, entire, raised, and red orange-colored after three days of incubation at 25℃ on R2A agar using seawater. Positive for esculin hydrolysis and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, and gelatinase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain IMCC34185 (=VYWGBAC000000119) was isolated from a tidal flat sample, Incheon, Korea.

Description of Gemmobacter lanyuensis IMCC34207

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, entire, convex, and cream-colored after three days of incubation at 25℃ on R2A agar using seawater. Positive for nitrate reduction, esculin hydrolysis, and arginine dihydrolase, urease, and β-galactosidase activity. Negative for indole production, glucose fermentation, and gelatinase activity. Utilizes d-mannitol, d-maltose, malic acid, and phenylacetic acid. Does not utilize d-glucose, l-arabinose, d-mannose, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, and trisodium citrate. Strain IMCC34207 (=VYWGBAC000000118) was isolated from a sand sample, Wando, Korea.

Description of Thalassospira lucentensis IMCC34233

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, entire, convex, and cream beige-colored after three days of incubation at 25℃ on R2A agar using seawater. Positive for esculin hydrolysis. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, and potassium gluconate. Does not utilize d-maltose, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain IMCC34233 (=VYWGBAC000000125) was isolated from a sand sample, Wando, Korea.

Description of Stappia stellulata GH4-12

Cells are gram-staining-negative, flagellated, and rod-shaped. Colonies are circular, entire, convex, and cream-colored after five days of incubation at 30℃ on MA. Negative for nitrate reduction, indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain GH4-12 (=VYWGBAC000000059) was isolated from a tidal flat sample, Incheon, Korea.

Description of Thioclava atlantica GH1-7

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, entire, convex, and creamcolored after five days of incubation at 30℃ on MA. Negative for nitrate reduction, indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Utilizes d-Mannitol. Does not utilize d-glucose, l-arabinose, d-mannose, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain GH1-7 (=VYWGBAC000000064) was isolated from a tidal flat sample, Incheon, Korea.

Description of Erythrobacter longus GH1-10

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, entire, convex, and orange-colored after five days of incubation at 30℃ on MA. Positive for esculin hydrolysis. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain GH1-10 (=VYWGBAC000000065) was isolated from a tidal flat sample, Incheon, Korea.

Description of Martelella radicis GH2-6

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are irregular, entire, convex, and cream-colored after five days of incubation at 30℃ on MA. Positive for esculin hydrolysis and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, and gelatinase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain GH2-6 (=VYWGBAC000000066) was isolated from a salt plant sample, Incheon, Korea.

Description of Pseudochrobactrum saccharolyticum Ibu_S_3

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, and cream-colored after three days of incubation at 30℃ on R2A agar. Positive for nitrate reduction, esculin hydrolysis, and gelatinase and β-galactosidase activity. Negative for indole production, glucose fermentation, and arginine dihydrolas and urease activity. Utilizes d-Glucose, d-mannose, N-acetyl-glucosamine, malic acid, and trisodium citrate. Does not utilize l-arabinose, d-mannitol, d-maltose, potassium gluconate, capric acid, adipic acid, and phenylacetic acid. Strain Ibu_ S_3 (=VYWGBAC000000108) was isolated from a soil sample, Anseong, Korea.

Description of Inquilinus limosus MMS17-GJ036

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are Irregular, convex, glistening, watery, and translucent beige-colored after three days of incubation at 30℃ on ISP 2 agar. Positive for esculin hydrolysis and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation and arginine dihydrolase, urease, and gelatinase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, malic acid, and trisodium citrate. Does not utilize capric acid, adipic acid, and phenylacetic acid. Strain MMS17- GJ036 (=VYWGBAC000000228) was isolated from a soil sample, Daejeon, Korea.

Description of Ensifer meliloti MMS17-SY214

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, entire, glistening, and beige-colored after three days of incubation at 30℃ on MA. Positive for esculin hydrolysis and urease, gelatinase, and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose and malic acid. Does not utilize potassium gluconate, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. Strain MMS17-SY214 (=VYWGBAC000000226) was isolated from a soil sample, Gunsan, Korea.

Description of Devosia insulae Gsoil1028

Cells are gram-staining-negative, flagellated, and ovoidshaped. Colonies are circular, raised, and white-colored after two days of incubation at 30℃ on R2A agar. Positive for esculin hydrolysis and gelatinase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain Gsoil 1028 (=VYWGBAC000000011) was isolated from a soil sample, Pocheon, Korea.

Description of Mesorhizobium qingshengii Gsoil 1111

Cells are gram-staining-negative, flagellated, and ovoidshaped. Colonies are circular, convex, smooth, glistening, and white-colored after two days of incubation at 30℃ on R2A agar. Positive for esculin hydrolysis. Negative for nitrate reduction, indole production, glucose fermentation, arginine dihydrolase, and urease, gelatinase, and β-galactosidase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, adipic acid, malic acid, and phenylacetic acid. Does not utilize d-maltose, capric acid, and trisodium citrate. Strain Gsoil 1111 (=VYWGBAC000000012) was isolated from a soil sample, Pocheon, Korea.

Description of Mesorhizobium tamadayense Gsoil318-1

Cells are gram-staining-negative, non-flagellated, and ovoid-shaped. Colonies are circular, raised, and white-colored after two days of incubation at 30℃ on R2A agar. Positive for esculin hydrolysis. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, gelatinase and β-galactosidase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, and d-maltose. Does not utilize potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain Gsoil318-1 ( =VYWGBAC000000023) was isolated from a soil sample, Pocheon, Korea.

Description of Devosia neptuniae Gsoil 824

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, smooth, glistening, and cream-colored after two days of incubation at 30℃ on R2A agar. Positive for urease activity. Negative for nitrate reduction, indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, gelatinase, and β-galactosidase activity. Utilizes N-Acetyl-glucosamine and d-maltose. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain Gsoil 824 (=VYWGBAC000000008) was isolated from a soil sample, Pocheon, Korea.

Description of Roseomonas vinacea HMF7612

Cells are gram-staining-negative, non-flagellated, and coccobacillus-shaped. Colonies are circular, convex, smooth, and red-colored after three days of incubation at 30℃ on R2A agar. Negative for nitrate reduction, indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Utilizes adipic acid and malic acid. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, trisodium citrate, and phenylacetic acid. Strain HMF7612 (=VYWGBAC000000183) was isolated from a tree sample, Yongin, Korea.

Description of Novosphingobium guangzhouense HMF7644

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, smooth, and pale yellow-colored after three days of incubation at 30℃ on R2A agar. Positive for esculin hydrolysis and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, and gelatinase activity. Utilizes d-Glucose, l-arabinose, d-mannose, N-acetyl-glucosamine, d-maltose, potassium gluconate, malic acid and trisodium citrate. Does not utilize d-mannitol, capric acid, adipic acid, and phenylacetic acid. Strain HMF7644 (=VYWGBAC000000184) was isolated from a tree sample, Seoul, Korea.

Description of Devosia psychrophila HMF7868

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, smooth, and whitecolored after three days of incubation at 30℃ on R2A agar. Positive for esculin hydrolysis and urease and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase and gelatinase activity. d-Glucose, l-arabinose, d-mannose, d-mannitol, and d-maltose are utilized. Does not utilize N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain HMF7868 (=VYWGBAC 000000186) was isolated from a tree sample, Yongin, Korea.

Description of Nesiotobacter exalbescens HMF8042

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, smooth, and whitecolored after three days of incubation at 30℃ on MA. Positive for indole production, glucose fermentation, and urease activity. Negative for nitrate reduction, esculin hydrolysis, and arginine dihydrolase, gelatinase, and β-galactosidase activity. Utilizes d-Glucose, d-mannose, Nacetyl-glucosamine, d-maltose, potassium gluconate, and phenylacetic acid. Does not utilize l-arabinose, d-mannitol, capric acid, adipic acid, malic acid, and trisodium citrate. Strain HMF8042 (=VYWGBAC000000189) was isolated from a water sample from a salt pond, Shinan, Korea.

Description of Stappia indica HMF8046

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, smooth, and pale orange-colored after three days of incubation at 30℃ on MA. Negative for nitrate reduction, indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, adipic acid, malic acid, trisodium citrate and phenylacetic acid. Does not utilize capric acid. Strain HMF8046 (=VYWGBAC000000191) was isolated from a water sample from a salt pond , Shinan, Korea.

Description of Roseibacterium beibuensis HMF8205

Cells are gram-staining-negative, non-flagellated, and short-ovoid to rod-shaped. Colonies are circular, convex, smooth, and pale red-colored after three days of incubation at 30℃ on MA. Positive for urease activity and esculin hydrolysis. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, gelatinase, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate and phenylacetic acid. Strain HMF8205 ( =VYWGBAC000000192) was isolated from a water sample from a salt pond, Shinan, Korea.

Description of Parvularcula oceanus HMF8467

Cells are gram-staining-negative, flagellated, and short rod-shaped. Colonies are circular, convex, smooth, and orange-colored after three days of incubation at 30℃ on MA. Positive for esculin hydrolysis and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, and gelatinase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain HMF8467 (=VYWGBAC000000193) was isolated from a water samples from a salt pond, Shinan, Korea.

Description of Palleronia abyssalis HMF8483

Cells are gram-staining-negative, non-flagellated, and short rod-shaped. Colonies are circular, convex, smooth, and pale red-colored after three days of incubation at 30℃ on MA. Positive for esculin hydrolysis and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, and gelatinase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, adipic acid, and malic acid. Does not utilize d-maltose, capric acid, trisodium citrate, and phenylacetic acid. Strain HMF8483 ( =VYWGBAC000000194) was isolated from a water sample from a salt pond, Shinan, Korea.

Description of Palleronia marisminoris HMF8486

Cells are gram-staining-negative, non-flagellated, and short rod-shaped. Colonies are circular, convex, smooth, and ivory-colored after three days of incubation at 30℃ on MA. Positive for esculin hydrolysis and urease and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase and gelatinase activity. Utilizes d-Glucose, l-arabinose, d-mannitol, d-maltose, and malic acid. Does not utilize d-mannose, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. Strain HMF8486 ( =VYWGBAC000000195) was isolated from a water sample from a salt pond, Shinan, Korea.

Description of Marinobacter salsuginis S-1

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are round, smooth, and white-colored after three days of incubation at 30℃ on MA. Positive for nitrate reduction and gelatinase activity. Negative for indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, urease, and β-galactosidase activity. Utilizes L-Arabinose, d-mannose, and capric acid. Does not utilize d-glucose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain S-1 (=VYWGBAC000000345) was isolated from a marine algae sample, Gangjin, Korea.

Description of Amylibacter lutimaris F-mm3

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are round, convex, smooth, and light yellow-colored after two days of incubation at 30℃ on MA. Positive for nitrate reduction, esculin hydrolysis, and urease and gelatinase activity. Negative for indole production, glucose fermentation, and arginine dihydrolase and β-galactosidase activity. Utilizes d-Glucose, d-mannose, d-mannitol, d-maltose, potassium gluconate, and malic acid. Does not utilize l-arabinose, N-acetyl-glucosamine, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. Strain F-mm3 (=VYWGBAC000000346) was isolated from a tidal flat sample, Asan, Korea.

Description of Altererythrobacter ishigakiensis StC2

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are round, smooth, and orange-col-ored after three days of incubation at 30℃ on MA. Positive for esculin hydrolysis. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, gelatinase, and β-galactosidase activity. Utilizes adipic acid and trisodium citrate. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, malic acid, and phenylacetic acid. Strain StC2 (=VYWGBAC000000350) was isolated from a red algae sample, Yeosu, Korea.

Description of Ralstonia pickettii BR3409

Cells are gram-staining-negative, non-flagellated, and ovoid rod-shaped. Colonies are circular, convex, hard, and yellow-colored incubation at 37℃ on R2A. Positive for esculin hydrolysis and urease and gelatinase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase and β-galactosidase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain BR3409 (=VYWGBAC000000172) was isolated from a butterfly (Hippoarchia autonoe) sample, Jeju, Korea.

Description of Massilia timonae JMn9

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, smooth, flat, entire, and pale yellow-colored after three days of incubation at 25℃ on R2A. Positive for esculin hydrolysis and urease, gelatinase, and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase activity. Utilizes l-Arabinose, d-mannose, d-maltose, malic acid, and trisodium citrate. Does not utilize d-glucose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, and phenylacetic acid. Strain JMn9 (=VYWGBAC000000143) was isolated from a tidal flat sample, Suncheon, Korea.

Description of Burkholderia dabaoshanensis WD42

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, smooth, convex, opaque, and ivory-colored after two days of incubation at 25℃ on R2A. Positive for nitrate reduction, glucose fermentation, esculin hydrolysis, and β-galactosidase activity. Negative for indole production and arginine dihydrolase, urease, and gelatinase activity. Utilizes d-Glucose, d-mannose, d-mannitol, N-acetyl-glucosamine, and malic acid. Does not utilize l-arabinose, d-maltose, potassium gluconate, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. Strain WD42 (=VYWGBAC000000148) was isolated from a soil sample, Wando, Korea.

Description of Paraburkholderia tropica Kw_8

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, and cream/pale yellow-colored after four days of incubation at 30℃ on R2A. Positive for glucose fermentation, esculin hydrolysis, and gelatinase and β-galactosidase activity. Negative for nitrate reduction, indole production, and arginine dihydrolase and urease activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, capric acid, malic acid, trisodium citrate, and phenylacetic acid. Does not utilize d-maltose and adipic acid. Strain Kw_8 (=VYWGBAC000000094) was isolated from a mud sample, Hwacheon, Korea.

Description of Paraburkholderia hospitaMMS17-GJ039

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, entire, smooth, and pale yellow-colored after three days of incubation at 30℃ on ISP 2 agar. Positive for esculin hydrolysis and β-galactosidase activity. Negative for nitrate reduction, indole production, glucose fermentation, and arginine dihydrolase, urease, and gelatinase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic. Does not utilize d-maltose. Strain MMS17-GJ039 ( =VYWGBAC000000242) was isolated from a soil sample, Daejeon, Korea.

Description of Paraburkholderia sartisoli Gsoil 096

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, entire, and cream-colored after two days of incubation at 30℃ on R2A. Positive for nitrate reduction. Negative for indole production, glucose fermentation, esculin hydrolysis and arginine dihydrolase, urease, and gelatinase β-galactosidase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, capric acid, malic acid, trisodium citrate, and phenylacetic acid. Does not utilize d-maltose and adipic acid. Strain Gsoil 096 (=VYWGBAC000000002) was isolated from a soil sample, Pocheon, Korea.

Description of Neisseria perflava HMF7346

Cells are gram-staining-negative, non-flagellated, and cocci chain-shaped. Colonies are circular, convex, smooth, and pale yellow-colored after four days of incubation at 30℃ on R2A. Positive for glucose fermentation. Negative for nitrate reduction, indole production, esculin hydrolysis, and arginine dihydrolase, urease, gelati-nase, and β-galactosidase activity. Utilizes d-Glucose, and d-maltose. Does not utilize l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain HMF7346 ( =VYWGBAC000000182) was isolated from a soil sample, Yongin, Korea

Description of Burkholderia peredens HMF7693

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, smooth, and white-colored after three days of incubation at 30℃ on R2A. Positive for arginine dihydrolase and urease activity. Negative for nitrate reduction, indole production, glucose fermentation, esculin hydrolysis, and gelatinase and β-galactosidase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, potassium gluconate, capric acid, malic acid, trisodium citrate, and phenylacetic acid. Does not utilize d-maltose and adipic acid. Strain HMF7693 (=VYWGBAC000000185) was isolated from a tree sample, Yongin, Korea

Description of Amantichitinum ursilacus HMF7887

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are wrinkled, hilly, wavy, and white-colored after three days of incubation at 30℃ on R2A. Positive for nitrate reduction, glucose fermentation, esculin hydrolysis, and β-galactosidase activity. Negative for indole production and arginine dihydrolase, urease and gelatinase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, and potassium gluconate. Does not utilize capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain HMF7887 (=VYWGBAC000000188) was isolated from a tree sample, Boseong, Korea

Description of Amantichitinum ursilacus HMF7887

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are wrinkled, hilly, wavy, and white-colored after three days of incubation at 30℃ on R2A. Positive for nitrate reduction, glucose fermentation, esculin hydrolysis, and β-galactosidase activity. Negative for indole production and arginine dihydrolase, urease, and gelatinase activity. Utilizes d-Glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, and potassium gluconate. Does not utilize capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain HMF7887 (=VYWGBAC000000188) was isolated from a tree sample, Boseong, Korea

Description of Uliginosibacterium paludis HMF4721

Cells are gram-staining-negative, non-flagellated, and rod-shaped. Colonies are circular, convex, smooth, and pale yellow-colored after three days of incubation at 30℃ on R2A. Positive for nitrate reduction and urease activity. Negative for indole production, glucose fermentation, esculin hydrolysis, and arginine dihydrolase, gelatinase, and β-galactosidase activity. Utilizes d-Glucose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate and malic acid. Does not utilize l-arabinose, d-mannose, capric acid, adipic acid, trisodium citrate, and phenylacetic acid. Strain HMF4721 ( =VYWGBAC000000180) was isolated from a water sample from a wetland, Yongin, Korea

Description of Halodesulfovibrio marinisediminis LPB0172

Cells are gram-staining-negative, non-flagellated, and cocci-shaped. Colonies are circular, convex, smooth, and black-colored after three days of incubation at 30℃ on MA. Negative for nitrate reduction, indole production, glucose fermentation, arginine dihydrolase, urease activity, esculin hydrolysis, gelatinase, and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate and phenylacetic acid. Strain LPB0172 (=VYWGBAC000000030) was isolated from a seawater sample, Incheon, Korea

Description of Arcobacter bivalviorum LPB0305

Cells are gram-staining-negative, flagellated, and rodshaped. Colonies are circular, convex, smooth, and whitecolored after 3 days of incubation at 25℃ on MA. Positive for nitrate reduction. Negative for indole production, glucose fermentation, esculin hydrolysis and arginine dihydrolase, urease, gelatinase and β-galactosidase activity. Does not utilize d-glucose, l-arabinose, d-mannose, d-mannitol, N-acetyl-glucosamine, d-maltose, potassium gluconate, capric acid, adipic acid, malic acid, trisodium citrate, and phenylacetic acid. Strain LPB0305 (=VYWGBAC000000046) was isolated from a seawater sample, Incheon, Korea